R Script for work

quickly install github R package

C:\Windows\System32\drivers\etc\hosts

git config --global http.sslBackend "openssl"

git config --global http.sslCAInfo C:/Program Files/R/R-3.6.0/library/openssl/cacert.pem

git config --global http.sslCAInfo /mnt/ilustre/centos7users/dna/.env/lib/R/library/openssl/cacert.pem

Build R Package

install packages from the github library("usethis") git_sitrep() # git situation report usethis::create_github_token()# open the website and make new token usethis::edit_r_environ() #可以改变temp的目录，重启就可以更新path #get tempdir ： tempdir()

#EDIT：GITHUB_TOKEN="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" #• Modify '/mnt/ilustre/users/meng.luo/.Renviron' #• Restart R for changes to take effect

Open-source packages can be installed directly and do not require the installation method mentioned above.

Sys.unsetenv("GITHUB_TOKEN")

If the installation package is too large, directly download the link from the error message, then install it locally.

setting time ： options(timeout = 600000000) ### set this to avoid timeout error

git config --global user.email "czheluo@gmail.com"

git config --global user.name "czheluo" conda install R need change the gun++11 to c++11, and need change install pkg-config (conda install ) conda install -c conda-forge pkg-config conda install -c anaconda hdf5

$ ./configure --prefix=/mnt/ilustre/users/czheluo/project/RNA/ST/R4.3.3 $ make $ make install

Miniconda3 install R

ADD CONDA-FORGE

$ conda config --add channels conda-forge

$ conda config --set channel_priority strict

INSTALL

$ conda search r-base

$ conda create -n R4.2.2

$ conda activate R4.2.2

$ conda install -c conda-forge -r r-base=4.2.2

INSTALL PACKAGES

$conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free

$conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

$conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda

$conda config --set show_channel_urls yes

host

reference

Schulze S, Henkel SG, Driesch D, Guthke R, Linde J. Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. Front Microbiol. 2015;6:65. Published 2015 Feb 6. doi:10.3389/fmicb.2015.00065

Read sequences along the indicated segments of the AB genome. Read counts (in brackets), read length and genomic position are indicated.

igraph for network from expression data

Chord Diagram

barplot